[gmx-users] Position restrained energy minimization

[Quyen Vu]

When you run EM with -v directive, you will see how much is the largest
force value applies to your atom. Try to estimate whether that force
constant was enough to keep your atom fix because if your structure has any
overlap, force can be very large

On Thu, Feb 7, 2019 at 6:40 AM Ashraya Ravikumar <ashrayar at gmail.com> wrote:

> Hi,
>
> I am trying to do position restrained energy minimization of a solvated
> peptide, where the peptide is restrained but the solvent is free to move.
> But I do see the positions of the atoms of the peptide change. I increased
> the force value in position restraint file to 10000 from 1000, but it
> doesn't help. It is important for my analysis that the internal bond
> parameters (bond lengths, angles, and torsion angle) of the peptide do not
> change from its initial values. Is there any solution for this?
>
> Thanks in advance.
>
> Regards,
> Ashraya
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